Holly Simon

Holly Simon

Associate Professor
Institute of Environmental Health; Division of Environmental and Biomolecular Systems
Affiliate Scientist, Center for Coastal Margin Observation and Prediction
Office: Hatfield Research Center, 3rd floor, Room 356
Phone: 503-346-3422
Website: Simon Research Group


B.S., (magna cum laude) Biology/Chemistry, Metropolitan State College of Denver, Colorado
Ph.D., Bacteriology, University of Wisconsin-Madison, 1996



  • University of Wisconsin-Madison, Department of Plant pathology; Research Associate 1996-2000, Assistant Scientist, 2000-2004
  • OHSU/OGI School of Science & Technology, Visiting Assistant Professor, Department of Environmental and Biolecular Systems, 2004


Research Interests

Projects in the lab cover a range of topics in microbial ecology, including the study of bacteria and archaea involved in carbon and nitrogen biogeochemical cycles, identification/monitoring of sentinels for environmental change, and remediation of environmental contaminants.


Selected Publications

Richard L. Johnson; Christina N. Brow; Reid O'Brien Johnson; Holly M. Simon
Cryogenic core collection and preservation of subsurface samples for biomolecular analysis
Groundwater Monitoring and Remediation. 2013;33(2):38-43.

S.L. Bräuer; K. Kranzler; N. Goodson; D. Murphy; H.M. Simon; A.M. Baptista; B.M. Tebo
Dark Carbon Fixation in the Columbia River's Estuarine Turbidity Maxima: Molecular Characterization of Red-Type cbbL Genes and Measurement of DIC Uptake Rates in Response to Added Electron Donors
Estuaries and Coasts. 2013;36(5):1073-1083.

Maria W. Smith; Lisa Zeigler Allen; Andrew E. Allen; Lydie Herfort; Holly M. Simon
Contrasting genomic properties of free-living and particle-attached microbial assemblages within a coastal ecosystem

Frontiers in Microbiology. 2013;4(MAY).

Christina N. Brow; Reid O'Brien Johnson; Richard L. Johnson; Holly M. Simon
Assessment of anaerobic toluene biodegradation activity by bssA transcript/gene ratios
Applied and Environmental Microbiology. 2013;79(17):5338-5344.

Mouzhong Xu; Jon Schnorr; Brandon Keibler; Holly M. Simon
Comparative analysis of 16S rRNA and amoA Genes from archaea selected with organic and inorganic amendments in enrichment culture
Applied and Environmental Microbiology. 2012;78(7):2137-2146.

Andrei L. Ghindilis; Maria W. Smith; Dean S. Messing; Vena N. Haynes; George B. Middleton; Kevin R. Schwarzkopf; Carmen E. Campbell; Changqing Zhan; Bruce Ulrich; Michael J. Frasier; et al.
Development of real-time assays for impedance-based detection of microbial double-stranded DNA targets: Optimization and data analysis
Biosensors and Bioelectronics. 2012;35(1):87-93.

Maria W. Smith; Michelle A. Maier; Dominic Suciu; Tawnya D. Peterson; Tyler Bradstreet; Jordan Nakayama; Holly M. Simon
High resolution microarray assay for rapid taxonomic assessment of Pseudo-nitzschia spp. (Bacillariophyceae) in the field
Harmful Algae. 2012;19:169-180.

S.L. Bräuer; C. Adams; K. Kranzler; D. Murphy; M. Xu; P. Zuber; H.M. Simon; A.M. Baptista; B.M. Tebo
Culturable Rhodobacter and Shewanella species are abundant in estuarine turbidity maxima of the Columbia River
Environmental Microbiology. 2011;13(3):589-603.

Adrin A. Pinto-Tomás; Ana Sittenfeld; Lorena Uribe-Lorío; Felipe Chavarría; Marielos Mora; Daniel H. Janzen; Robert M. Goodman; Holly M. Simon
Comparison of Midgut Bacterial Diversity in Tropical Caterpillars (Lepidoptera: Saturniidae) Fed on Different Diets
Environmental Entomology. 2011;40(5):1111-1122.

Andrey L. Ghindilis; Kevin R. Schwarzkopf; Dean S. Messing; Ibrahim Sezan; Paul Schuele; Changqing Zhan; Maria W. Smith; Holly M. Simon; David R. Evans
Real-time biosensor platform: Fully integrated device for impedimetric assays
ECS Transactions. 2010;33(8):59-68.

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